Removing ohif-cornerstone as a dependency for ohif-viewerbase (Final step)
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Eloízio Salgado authored and Emanuel F. Oliveira committed
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import { parsingUtils } from '../parsingUtils';
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export class MetadataProvider {
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constructor() {
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this.metadataLookup = {};
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}
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/**
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* Cornerstone Metadata provider to store image meta data
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* Data from instances, series, and studies are associated with
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* imageIds to facilitate usage of this information by Cornerstone's Tools
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*
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* e.g. the imagePlane metadata object contains instance information about
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* row/column pixel spacing, patient position, and patient orientation. It
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* is used in CornerstoneTools to position reference lines and orientation markers.
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*
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* @param {String} imageId The Cornerstone ImageId
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* @param {Object} data An object containing instance, series, and study metadata
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*/
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addMetadata(imageId, data) {
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const instanceMetadata = data.instance;
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const seriesMetadata = data.series;
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const studyMetadata = data.study;
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const imageIndex = data.imageIndex;
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const numImages = data.numImages;
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const metadata = {};
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metadata.study = {
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patientId: studyMetadata.patientId,
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studyInstanceUid: studyMetadata.studyInstanceUid,
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studyDate: studyMetadata.studyDate,
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studyTime: studyMetadata.studyTime,
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studyDescription: studyMetadata.studyDescription,
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institutionName: studyMetadata.institutionName,
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patientHistory: studyMetadata.patientHistory
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};
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metadata.series = {
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seriesDescription: seriesMetadata.seriesDescription,
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seriesNumber: seriesMetadata.seriesNumber,
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modality: seriesMetadata.modality,
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seriesInstanceUid: seriesMetadata.seriesInstanceUid,
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numImages: numImages
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};
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metadata.instance = instanceMetadata;
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metadata.patient = {
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name: studyMetadata.patientName,
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id: studyMetadata.patientId,
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birthDate: studyMetadata.patientBirthDate,
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sex: studyMetadata.patientSex
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};
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// If there is sufficient information, populate
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// the imagePlane object for easier use in the Viewer
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metadata.imagePlane = this.getImagePlane(instanceMetadata);
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// Add the metadata to the imageId lookup object
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this.metadataLookup[imageId] = metadata;
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}
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/**
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* Adds a set of metadata to the Cornerstone metadata provider given a specific
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* imageId, type, and dataset
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*
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* @param imageId
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* @param type (e.g. series, instance, tagDisplay)
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* @param data
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*/
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addSpecificMetadata(imageId, type, data) {
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const metadata = {};
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metadata[type] = data;
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this.metadataLookup[imageId] = $.extend(this.metadataLookup[imageId], metadata);
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}
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getFromDataSet(dataSet, type, tag) {
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if (!dataSet) {
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return;
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}
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const fn = dataSet[type];
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if (!fn) {
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return;
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}
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return fn.call(dataSet, tag);
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}
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/**
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* Updates the related metadata for missing fields given a specified image
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*
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* @param image
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*/
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updateMetadata(image) {
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const imageMetadata = this.metadataLookup[image.imageId];
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if (!imageMetadata) {
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return;
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}
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imageMetadata.instance.rows = imageMetadata.instance.rows || image.rows;
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imageMetadata.instance.columns = imageMetadata.instance.columns || image.columns;
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imageMetadata.instance.sopClassUid = imageMetadata.instance.sopClassUid || this.getFromDataSet(image.data, 'string', 'x00080016');
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imageMetadata.instance.sopInstanceUid = imageMetadata.instance.sopInstanceUid || this.getFromDataSet(image.data, 'string', 'x00080018');
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imageMetadata.instance.pixelSpacing = imageMetadata.instance.pixelSpacing || this.getFromDataSet(image.data, 'string', 'x00280030');
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imageMetadata.instance.frameOfReferenceUID = imageMetadata.instance.frameOfReferenceUID || this.getFromDataSet(image.data, 'string', 'x00200052');
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imageMetadata.instance.imageOrientationPatient = imageMetadata.instance.imageOrientationPatient || this.getFromDataSet(image.data, 'string', 'x00200037');
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imageMetadata.instance.imagePositionPatient = imageMetadata.instance.imagePositionPatient || this.getFromDataSet(image.data, 'string', 'x00200032');
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imageMetadata.instance.sliceThickness = imageMetadata.instance.sliceThickness || this.getFromDataSet(image.data, 'string', 'x00180050');
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imageMetadata.instance.sliceLocation = imageMetadata.instance.sliceLocation || this.getFromDataSet(image.data, 'string', 'x00201041');
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imageMetadata.instance.tablePosition = imageMetadata.instance.tablePosition || this.getFromDataSet(image.data, 'string', 'x00189327');
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imageMetadata.instance.spacingBetweenSlices = imageMetadata.instance.spacingBetweenSlices || this.getFromDataSet(image.data, 'string', 'x00180088');
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imageMetadata.instance.lossyImageCompression = imageMetadata.instance.lossyImageCompression || this.getFromDataSet(image.data, 'string', 'x00282110');
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imageMetadata.instance.lossyImageCompressionRatio = imageMetadata.instance.lossyImageCompressionRatio || this.getFromDataSet(image.data, 'string', 'x00282112');
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imageMetadata.instance.frameIncrementPointer = imageMetadata.instance.frameIncrementPointer || this.getFromDataSet(image.data, 'string', 'x00280009');
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imageMetadata.instance.frameTime = imageMetadata.instance.frameTime || this.getFromDataSet(image.data, 'string', 'x00181063');
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imageMetadata.instance.frameTimeVector = imageMetadata.instance.frameTimeVector || this.getFromDataSet(image.data, 'string', 'x00181065');
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if (image.data && !imageMetadata.instance.multiframeMetadata) {
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imageMetadata.instance.multiframeMetadata = this.getMultiframeModuleMetadata(image.data);
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}
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imageMetadata.imagePlane = imageMetadata.imagePlane || this.getImagePlane(imageMetadata.instance);
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}
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/**
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* Constructs and returns the imagePlane given the metadata instance
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*
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* @param metadataInstance The metadata instance (InstanceMetadata class) containing information to construct imagePlane
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* @returns imagePlane The constructed imagePlane to be used in viewer easily
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*/
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getImagePlane(instance) {
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if (!instance.rows || !instance.columns || !instance.pixelSpacing ||
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!instance.frameOfReferenceUID || !instance.imageOrientationPatient ||
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!instance.imagePositionPatient) {
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return;
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}
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const imageOrientation = instance.imageOrientationPatient.split('\\');
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const imagePosition = instance.imagePositionPatient.split('\\');
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let columnPixelSpacing = 1.0;
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let rowPixelSpacing = 1.0;
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if (instance.pixelSpacing) {
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const split = instance.pixelSpacing.split('\\');
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rowPixelSpacing = parseFloat(split[0]);
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columnPixelSpacing = parseFloat(split[1]);
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}
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return {
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frameOfReferenceUID:
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instance.frameOfReferenceUID,
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rows:
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instance.rows,
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columns:
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instance.columns,
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rowCosines:
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new cornerstoneMath.Vector3(parseFloat(imageOrientation[0]), parseFloat(imageOrientation[1]), parseFloat(imageOrientation[2])),
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columnCosines:
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new cornerstoneMath.Vector3(parseFloat(imageOrientation[3]), parseFloat(imageOrientation[4]), parseFloat(imageOrientation[5])),
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imagePositionPatient:
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new cornerstoneMath.Vector3(parseFloat(imagePosition[0]), parseFloat(imagePosition[1]), parseFloat(imagePosition[2])),
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rowPixelSpacing:
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rowPixelSpacing,
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columnPixelSpacing:
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columnPixelSpacing,
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};
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}
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/**
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* This function extracts miltiframe information from a dicomParser.DataSet object.
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*
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* @param dataSet {Object} An instance of dicomParser.DataSet object where multiframe information can be found.
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* @return {Object} An object containing multiframe image metadata (frameIncrementPointer, frameTime, frameTimeVector, etc).
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*/
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getMultiframeModuleMetadata(dataSet) {
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const imageInfo = {
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isMultiframeImage: false,
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frameIncrementPointer: null,
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numberOfFrames: 0,
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frameTime: 0,
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frameTimeVector: null,
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averageFrameRate: 0 // backwards compatibility only... it might be useless in the future
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};
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let frameTime;
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if (parsingUtils.isValidDataSet(dataSet)) {
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// (0028,0008) = Number of Frames
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const numberOfFrames = dataSet.intString('x00280008', -1);
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if (numberOfFrames > 0) {
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// set multi-frame image indicator
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imageInfo.isMultiframeImage = true;
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imageInfo.numberOfFrames = numberOfFrames;
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// (0028,0009) = Frame Increment Pointer
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const frameIncrementPointer = parsingUtils.attributeTag(dataSet, 'x00280009') || '';
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if (frameIncrementPointer === 'x00181065') {
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// Frame Increment Pointer points to Frame Time Vector (0018,1065) field
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const frameTimeVector = parsingUtils.floatArray(dataSet, 'x00181065');
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if (frameTimeVector instanceof Array && frameTimeVector.length > 0) {
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imageInfo.frameIncrementPointer = 'frameTimeVector';
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imageInfo.frameTimeVector = frameTimeVector;
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frameTime = frameTimeVector.reduce((a, b) => a + b) / frameTimeVector.length;
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imageInfo.averageFrameRate = 1000 / frameTime;
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}
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} else if (frameIncrementPointer === 'x00181063' || frameIncrementPointer === '') {
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// Frame Increment Pointer points to Frame Time (0018,1063) field or is not defined (for addtional flexibility).
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// Yet another value is possible for this field (5200,9230 for Multi-frame Functional Groups)
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// but that case is currently not supported.
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frameTime = dataSet.floatString('x00181063', -1);
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if (frameTime > 0) {
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imageInfo.frameIncrementPointer = 'frameTime';
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imageInfo.frameTime = frameTime;
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imageInfo.averageFrameRate = 1000 / frameTime;
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}
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}
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}
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}
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return imageInfo;
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}
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/**
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* Looks up metadata for Cornerstone Tools given a specified type and imageId
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* A type may be, e.g. 'study', or 'patient', or 'imagePlane'. These types
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* are keys in the stored metadata objects.
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*
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* @param type
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* @param imageId
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* @returns {Object} Relevant metadata of the specified type
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*/
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provider(type, imageId) {
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const imageMetadata = this.metadataLookup[imageId];
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if (!imageMetadata) {
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return;
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}
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if (imageMetadata.hasOwnProperty(type)) {
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return imageMetadata[type];
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}
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}
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};
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